Mercurial > repos > ebi-gxa > monocle3_plotcells

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/monocle3-macros.xml	Mon Sep 16 09:51:16 2019 -0400
@@ -0,0 +1,64 @@
+<macros>
+  <token name="@TOOL_VERSION@">0.1.2</token>
+  <token name="@HELP@">More information can be found at https://cole-trapnell-lab.github.io/monocle3/ and https://github.com/ebi-gene-expression-group/monocle-scripts</token>
+  <token name="@VERSION_HISTORY@"><![CDATA[
+**Version history**
+
+0.1.2+galaxy0: Initial version based on monocle3-cli 0.0.3 and monocle3 0.1.2
+    ]]></token>
+  <token name="@INPUT_OPTS@">
+    --input-object-format '${input_object_format}' '${input_object_file}'
+  </token>
+  <token name="@OUTPUT_OPTS@">
+    --output-object-format '${output_object_format}' output.RDS
+#if $introspective
+    --introspective
+#end if
+  </token>
+  <token name="@VERBOSE@">
+#if $verbose
+    --verbose
+#end if
+  </token>
+
+  <xml name="requirements">
+    <requirements>
+      <requirement type="package" version="0.0.3">monocle3-cli</requirement>
+      <yield/>
+    </requirements>
+  </xml>
+
+  <xml name="citations">
+    <citations>
+      <yield />
+      <citation type="doi">10.1038/nmeth.4402</citation>
+      <citation type="bibtex">
+	@misc{githubscanpy-scripts,
+	author = {Ni Huang, Krzysztof Polanski, EBI Gene Expression Team},
+	year = {2019},
+	title = {Monocle3-cli: command line interface for Monocle3},
+	publisher = {GitHub},
+	journal = {GitHub repository},
+	url = {https://github.com/ebi-gene-expression-group/monocle-scripts},
+      }</citation>
+    </citations>
+  </xml>
+
+  <xml name="input_object_params">
+    <param name="input_object_file" argument="input-object-file" type="data" format="rdata" label="Input object in RDS format"/>
+    <param name="input_object_format" argument="--input-object-format" type="select" label="Format of input object">
+      <option value="cds3" selected="true">Monocle3 object in RDS</option>
+    </param>
+  </xml>
+
+  <xml name="output_object_params">
+    <param name="output_object_format" argument="--output-object-format" type="select" label="Format of output object">
+      <option value="cds3" selected="true">Monocle3 object in RDS</option>
+    </param>
+    <param name="introspective" argument="--introspective" type="boolean" checked="true" label="Print introspective information of output object"/>
+  </xml>
+
+  <xml name="verbose_flag">
+  	<param name="verbose" argument="--verbose" type="boolean" checked="false" label="Emit verbose output"/>
+  </xml>
+</macros>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/monocle3-plotCells.xml	Mon Sep 16 09:51:16 2019 -0400
@@ -0,0 +1,114 @@
+<?xml version="1.0" encoding="utf-8"?>
+<tool id="monocle3_plotCells" name="Monocle3 plotCells" version="@TOOL_VERSION@+galaxy0">
+  <description> in the reduced dimensionality space</description>
+  <macros>
+    <import>monocle3-macros.xml</import>
+  </macros>
+  <expand macro="requirements"/>
+  <command detect_errors="exit_code"><![CDATA[
+LANG=en_US.UTF-8 monocle3 plotCells
+    --reduction-method '$(reduction_method)'
+    --norm-method '$(norm_method)'
+#if $xdim
+    --xdim '$(xdim)'
+#end if
+#if $ydim
+    --ydim '$(ydim)'
+#end if
+#if $color_cells_by
+    --color-cells-by '$(color_cells_by)'
+#end if
+#if $genes
+    --genes '$(genes)'
+#end if
+#if $cell_size
+    --cell-size '$(cell_size)'
+#end if
+#if $alpha
+    --alpha '$(alpha)'
+#end if
+#if $label_cell_groups
+    --label-cell-groups
+#end if
+#if $no_trajectory_graph
+    --no-trajectory-graph
+#end if
+#if $label_groups_by_cluster
+    --label-groups-by-cluster
+#end if
+#if $label_leaves
+    --label-leaves
+#end if
+#if $label_roots
+    --label-roots
+#end if
+#if $label_branch_points
+    --label-branch-points
+#end if
+
+    @INPUT_OPTS@
+    output.png
+
+    @VERBOSE@
+]]></command>
+
+  <inputs>
+    <expand macro="input_object_params"/>
+    <param name="xdim" argument="--xdim" optional="true" type="integer" value="1" label="The column of reducedDimS(cds) to plot on the horizontal axis."/>
+    <param name="ydim" argument="--ydim" optional="true" type="integer" value="2" label="The column of reducedDimS(cds) to plot on the vertical axis."/>
+    <param name="reduction_method" argument="--reduction-method" type="select" label="The dimensionality reduction for plotting.">
+      <option value="UMAP" selected="true">UMAP</option>
+      <option value="tSNE">tSNE</option>
+      <option value="PCA">PCA</option>
+      <option value="LSI">LSI</option>
+    </param>
+    <param name="color_cells_by" argument="--color-cells-by" optional="true" type="text" value="pseudotime" label="The cell attribute (e.g. the column of pData(cds)) to map to each cell's color, or one of {cluster, partition, pseudotime}."/>
+    <param name="genes" argument="--genes" optional="true" type="text" label="A list of gene IDs/short names to plot, one per panel."/>
+    <param name="norm_method" argument="--norm-method" type="select" label="Determines how to transform expression values for plotting.">
+      <option value="log" selected="true">Size factor correction and log transformation</option>
+      <option value="size_only">Size factor correction only</option>
+    </param>
+    <param name="cell_size" argument="--cell-size" optional="true" type="float" value="1.5" label="The size of the point for each cell."/>
+    <param name="alpha" argument="--alpha" optional="true" type="float" value="1" label="The alpha aesthetics for the original cell points, useful to highlight the learned principal graph."/>
+    <param name="label_cell_groups" argument="--label-cell-groups" type="boolean" checked="true" label="If set, display the cell group names directly on the plot. Otherwise include a color legend on the side of the plot."/>
+    <param name="no_trajectory_graph" argument="--no-trajectory-graph" type="boolean" checked="false" label="When this option is set, skip displaying the trajectory graph inferred by learn_graph()."/>
+    <param name="label_groups_by_cluster" argument="--label-groups-by-cluster" type="boolean" checked="false" label="If set, and setting --color-cells-by to something other than cluster, label the cells of each cluster independently. Can result in duplicate labels being present in the manifold."/>
+	<param name="label_leaves" argument="--label-leaves" type="boolean" checked="false" label="If set, label the leaves of the principal graph."/>
+	<param name="label_roots" argument="--label-roots" type="boolean" checked="false" label="If set, label the roots of the principal graph."/>
+	<param name="label_branch_points" argument="--label-branch-points" type="boolean" checked="false" label="If set, label the branch points of the principal graph."/>
+    <expand macro="verbose_flag"/>
+  </inputs>
+
+  <outputs>
+    <data name="output_tsv" format="png" from_work_dir="output.png" label="${tool.name} on ${on_string}: png"/>
+  </outputs>
+
+  <tests>
+    <test>
+      <param name="input_object_file" value="input.RDS"/>
+      <param name="input_object_format" value="cds3"/>
+      <param name="reduction_method" value="UMAP"/>
+      <param name="xdim" value="1"/>
+      <param name="ydim" value="2"/>
+      <param name="color_cells_by" value="pseudotime"/>
+      <param name="norm_method" value="log"/>
+      <param name="cell_size" value="1.5"/>
+      <param name="alpha" value="1"/>
+      <output name="output_tsv" file="output.tsv" ftype="tsv" compare="sim_size"/>
+    </test>
+  </tests>
+
+  <help><![CDATA[
+=====================================
+Monocle3 cell plotting (`plot_cells`)
+=====================================
+
+Display various information about cells (clustering, pseudotime, the inferred graph,
+user-provided annotations, gene expression) in reduced dimensions.
+
+@HELP@
+
+@VERSION_HISTORY@
+]]></help>
+  <expand macro="citations"/>
+</tool>